Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RAD21

Cell type

Cell type Class
Bone
Cell type
A-673
Primary Tissue
Skeletal Muscle
Tissue Diagnosis
Rhabdomyosarcoma

Attributes by original data submitter

Sample

source_name
Ewing sarcoma cell line (A673)
cell line
A673
cell type
Ewing sarcoma cell line
genotype
SA2 KO
antibody
RAD21 (ab992, Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChiP were performed following manufacturer instructions using iDeal ChIP-seq kit for transcription factors and for histones (Diagenode). For this, Ewing cell lines were fixed for 10 minutes with 1% of methanol-free formaldehyde (28908, Thermo-Scientific). Chromatin was sonicated (Bioruptor, Diagenode) for 20 cycles (30-sec on, 30-sec off) set at position “high” to generate DNA fragments with an average size around 150-300pb. The library were constructed using TruSeq ChIP library preparation kit (Illumina) according to manufacturer recommendations

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
50699369
Reads aligned (%)
91.7
Duplicates removed (%)
26.7
Number of peaks
35784 (qval < 1E-05)

hg19

Number of total reads
50699369
Reads aligned (%)
90.7
Duplicates removed (%)
28.1
Number of peaks
35165 (qval < 1E-05)

Base call quality data from DBCLS SRA